Since 1987, we have examined over 100 DNA bases and nucleosides that are modified with carcinogenic polycyclic aromatic hydrocarbons (PAH). More recently, we have expanded the research to include potentially carcinogenic steroid hormones (e.g., estrogens). These materials share a chemical property with that of PAH; that is both materials cause modification and depurination of DNA. We are now using low energy collisional activation (on triple quadrupoles), and post-source decompositions (PSD) on MALDI/time-of-flight instruments as well as high-energy collisional activation as possible methods for extracting structural information from modified DNA. The goal is to understand the ion chemistry associated with the fragmentation, to provide insight on the mechanism of PSD, to evaluate the advantages and limitations of the various methods for inducing fragmentation in biomolecules, and to utilize the ion-trap mass spectrometer (Finnigan LCQ) in combination with HPLC i ntro duction for quantification and identification by MS/MS. Mass spectrometry has already been used to show that these catechol estrogens modify DNA and glutathione. The latter work offers the opportunity to examine whether there are biomarkers that indicate women at risk for breast cancer.